3NO9

Crystal Structure of apo fumarate hydratase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YFEPDB ENTRY 1YFE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.529318% PEG 400, 0.1M sodium acetate pH 4.5, 0.2M calcium chloride, drop ratio 1:1, protein concentration 8mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 271.224α = 90
b = 96.555β = 102.99
c = 89.889γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR2007-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4848.52388.50.1518.63.17073040.99
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.482.5971.90.4140.4142.392.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1YFE2.4848.521.917077370709353388.40.2080.2060.241
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.4885-2.1327-5.81356.302
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.364
f_angle_d1.058
f_chiral_restr0.072
f_bond_d0.008
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13421
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling